I think there is some confusion with the SJC and the Alice case. While business methods patents are not patentable just because they are put onto a computer system, WDDD patents are patentable.
The best part of the article, and John Gibson's explanation, is as follows from the posting, "SCOTUS did not rule that software or computer code in and of itself is too abstract to patent, but that the idea behind Alice's software was. Alice Corp. basically took a system that was already in use (escrow account for trade settlements) and computerized it. That would be like making a computer program for balancing a checkbook and patenting that."
The Alice case is different from the case with WDDD. Without a computer system, you can't do the things that the WDDD patent covers.